Data from: Genomic footprints of adaptation in a cooperatively breeding tropical bird across a vegetation gradient

Termignoni-Garcia F, Jaramillo-Correa JP, Chablé-Santos J, Liu M, Shultz AJ, Edwards SV, Escalante Pliego P

Date Published: June 28, 2017

DOI: https://doi.org/10.5061/dryad.2t6t8

Files in this package

Content in the Dryad Digital Repository is offered "as is." By downloading files, you agree to the Dryad Terms of Service. To the extent possible under law, the authors have waived all copyright and related or neighboring rights to this data. CC0 (opens a new window) Open Data (opens a new window)

Title Cy_FASTQ
Downloaded 11 times
Description FASTq sequences of 38 individuals used, with their corresponding barcode from the sequencing. See file "Cy_GENERAL-DATA-ID-GEO-CATALOG.txt" to know the general information of the samples.
Download Cy_samplesFASTQ.tar.gz (7.965 Gb)
Download README.txt (3.313 Kb)
Details View File Details
Title Cy_GENERAL-DATA-ID-GEO-CATALOG
Downloaded 9 times
Description General information of the 38 samples: catalog-voucher from the National Ornithology Collection (UNAM, Mexico), sample ID (barcodes from the sequencing) geographic position (longitude and latitude), the corresponding operative-geogaraphic-unit (OGU), vegetation type and number of the sampling point (see Figure 1 in the article).
Download Cy_GENERAL-DATA-ID-GEO-CATALOG.txt (2.118 Kb)
Download README.txt (3.313 Kb)
Details View File Details
Title Cy_Bioclim-Morpho
Downloaded 7 times
Description Bioclimatic and morphometric data of the 38 samples. In table are the Sample-ID/sequencing barcode, the corresponding operative-geographic-unit, six morphometric measures (WIL, TAL, TRL, CUL, BIW, BID) and all the 19 bioclimatic data obtained from WorldClim databases.
Download Cy_Bioclim-Morpho.txt (5.187 Kb)
Download README.txt (3.313 Kb)
Details View File Details
Title Cy_Gsnap-alignment
Downloaded 11 times
Description Sam files of the 38 individuals with two types of alignment to a Pseudo-Reference-Genome (PRG), to the American Crow (Cy_AmericanCrow) and the Zebra Finch (Cy_ZebraFinch), performed with Gsnap and after all filters (clone filter, optical duplicates and mapping quality).
Download Cy_Gsnap_alignment.tar.gz (169.7 Mb)
Download README.txt (3.313 Kb)
Details View File Details
Title Cy_STACKS_output
Downloaded 6 times
Description STACKS output from the correction module (rx_stacks) of ref_map (two PRG: PRG_AmericanCrow and PRG_ZebraFinch) and de_novo (run 1 and run 2 separate: Denovo_R1 and Denovo_R2) pipelines and populations maps used (Cy_2POP.txt and Cy_3POP.txt). Included are the catalog.tags, de-novo assemblies and output of the populations module. Each directory includes summary statistics per locus and overall, and all SNP data in STRUCTURE, FASTA, Genpop, PLINK and VCF format.
Download Cy_STACKS_output.tar.gz (35.53 Mb)
Download README.txt (3.313 Kb)
Details View File Details
Title Cy_LFMM_input
Downloaded 9 times
Description Input used in LFMM analyses including genetic (Cy.lfmm) and environmental (Cy.lfmm.env) data for each individual. The order of the samples are in file "ORDER-SAMPLES-plink-LFMM.txt"
Download Cy_LFMM_input.tar.gz (8.454 Kb)
Download README.txt (3.313 Kb)
Details View File Details
Title Cy_Baypass_input
Downloaded 6 times
Description Input used in BayPass analyses including genetic (Cy.BayPass2allele.count.txt) and environmental (Cy.BayPass-var-X.txt) data. The environmental data are in separate files for each of the final nine climatic variables used (e.g Cy.BayPass-var-bio4.txt). The order of the samples are in file "ORDER-SAMPLES-BayPass.txt".
Download Cy_Baypass_input.tar.gz (12.36 Kb)
Download README.txt (3.313 Kb)
Details View File Details
Title Cy_Bedassle
Downloaded 11 times
Description Input and output BEDASSLE files. Genetic data for each population are in the allele.counts and sample.sizes files. Environmental data matrices are located in the .csv files. Output is in R object files and statistic values in PARAM and INTERVALS .txt files. Files correspond to the candidate-SNPs and non-candidate-SNPS, per each allele 1 and allele 2 (A1 and A2) and their replicate run (Rep_A1 and Rep_A2).
Download Cy_Bedassle.tar.gz (149.9 Mb)
Download README.txt (3.313 Kb)
Details View File Details
Title Cy_Fasta_BLAST
Downloaded 15 times
Description FASTA file of consensus sequences containing all SNPs (CLOCUS_) used in the study and BLAST (MATCHCLOCUS and Q_Query=) results of these loci.
Download Cy_Fasta_BLAST.tar.gz (361.9 Kb)
Download README.txt (3.313 Kb)
Details View File Details

When using this data, please cite the original publication:

Termignoni-García F, Jaramillo-Correa JP, Chablé-Santos J, Liu M, Shultz AJ, Edwards SV, Escalante-Pliego P (2017) Genomic footprints of adaptation in a cooperatively breeding tropical bird across a vegetation gradient. Molecular Ecology 26(17): 4483-4496. https://doi.org/10.1111/mec.14224

Additionally, please cite the Dryad data package:

Termignoni-Garcia F, Jaramillo-Correa JP, Chablé-Santos J, Liu M, Shultz AJ, Edwards SV, Escalante Pliego P (2017) Data from: Genomic footprints of adaptation in a cooperatively breeding tropical bird across a vegetation gradient. Dryad Digital Repository. https://doi.org/10.5061/dryad.2t6t8
Cite | Share
Download the data package citation in the following formats:
   RIS (compatible with EndNote, Reference Manager, ProCite, RefWorks)
   BibTex (compatible with BibDesk, LaTeX)

Search for data

Be part of Dryad

We encourage organizations to: